scholarly journals Kinetic networks identify key regulatory nodes and transcription factor functions in early adipogenesis

2021 ◽  
Author(s):  
Arun B Dutta ◽  
Bao Ngyuen ◽  
Warren D Anderson ◽  
Ninad M Walavalkar ◽  
Fabiana M Duarte ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Activation ◽  
Compartment Model ◽  
Chromatin Accessibility ◽  
Regulate Gene Expression ◽  
Cellular Processes ◽  
Brown Adipose ◽  
Regulatory Cascades

Sequence-specific transcription factors (TFs) bind DNA, modulate chromatin structure, regulate gene expression, and orchestrate transcription cascades. Activation and repression of TFs drive tightly controlled regulatory programs that lead to cellular processes such as differentiation. We measured chromatin accessibility and nascent transcription at seven time points over the first four hours of induced adipogenesis of 3T3-L1 mouse preadipocytes to construct dynamic gene regulatory networks. Regulatory networks describe successive waves of TF binding and dissociation followed by direct regulation of proximal genes. We identified 14 families of TFs that coordinate with and antagonize each other to regulate early adipogenesis. We developed a compartment model to quantify individual TF contributions to RNA polymerase initiation and pause release rates. Network analysis showed that the glucocorticoid receptor and AP1 drive immediate gene activation, including induction of Twist2. Twist2 is a highly interconnected node within the network and its expression leads to repression of target genes. Although Twist2's role in adipogenesis has not been previously appreciated, both Twist2 knockout mice and Setleis syndrome (Twist2-/-) patients lack subcutaneous and brown adipose tissue. We found that kinetic networks integrating chromatin structure and nascent transcription dynamics identify key genes, TF functions, and coordinate interactions within regulatory cascades.

scholarly journals miRDRN – miRNA Disease Regulatory Network: A tool for exploring disease and tissue-specific microRNA regulatory networks

2019 ◽  
Author(s):  
Hsueh-Chuan Liu ◽  
Yi-Shian Peng ◽  
Hoong-Chien Lee
Keyword(s):  
Web Service ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Annotation ◽  
Service Platform ◽  
Tissue Specific ◽  
Cellular Processes ◽  
Specific Subset ◽  
Pathway Gene

Background. MiRNA regulates cellular processes through acting on specific target genes. Hundreds of miRNAs and their target genes have been identified, as are many miRNA-disease associations. Cellular processes, including those related to disease, proceed through multiple interactions, are often organized into pathways among genes and gene products. Large databases on protein-protein interactions (PPIs) are available. Here, we have integrated the information mentioned above to build a web service platform, miRNA Disease Regulatory Network, or miRDRN, for users to construct disease and tissue-specific miRNA-protein regulatory networks. Methods. Data on human protein interaction, disease-associated miRNA, tumor-associated gene, miRNA targeted gene, molecular interaction and reaction network or pathway, gene ontology, gene annotation and gene product information, and gene expression were collected from publicly available databases and integrated. A complete set of regulatory sub-pathways (RSPs) having the form (M, T, G1, G2) were built from the integrated data and stored in the database part of miRDRN, where M is a disease-associated miRNA, T is its regulatory target gene, G1 (G2) is a gene/protein interacting with T (G1). Each sequence (T, G1, G2) was assigned a p-value weighted by the participation of the three genes in molecular interactions and reaction pathways. Results. A web service platform, miRDRN ( http://mirdrn.ncu.edu.tw/mirdrn/), was built to allow users to retrieve a disease and tissue-specific subset of RSPs, from which a miRNA regulatory network is constructed. miRDRN is a database that currently contains 6,973,875 p-valued sub-pathways associated with 119 diseases in 78 tissue types built from 207 diseases-associated miRNA regulating 389 genes, and a web tool that facilitates the construction and visualization of disease and tissue-specific miRNA-protein regulatory networks, for exploring single diseases, or for exploring the comorbidity of disease-pairs. As demonstrations, miRDRN was applied: to explore the single disease colorectal cancer (CRC), in which 26 novel potential CRC target genes were identified; to study the comorbidity of the disease-pair Alzheimer's disease-Type 2 diabetes (AD-T2D), in which 18 novel potential comorbid genes were identified; and, to explore possible causes that may shed light on recent failures of late-phase trials of anti-AD, BACE1 inhibitor drugs, in which genes downstream to BACE1 whose suppression may affect signal transduction were identified.

FLT3ITD Target Enhancers Are Primed but Inaccessible in Fetal Hematopoietic Progenitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1228-1228
Author(s):  
Yanan Li ◽  
Riddhi M Patel ◽  
Emily Casey ◽  
Jeffrey A. Magee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Gene Activation ◽  
Chromatin Accessibility ◽  
Luciferase Reporter ◽  
Enhancer Activity ◽  
Target Gene Expression

The FLT3 Internal Tandem Duplication (FLT3ITD) is common somatic mutation in acute myeloid leukemia (AML). We have previously shown that FLT3ITD fails to induce changes in HSC self-renewal, myelopoiesis and leukemogenesis during fetal stages of life. FLT3ITD signal transduction pathways are hyperactivated in fetal progenitors, but FLT3ITD target genes are not. This suggests that postnatal-specific transcription factors may be required to help induce FLT3ITD target gene expression. Alternatively, repressive histone modifications may impose a barrier to FLT3ITD target gene activation in fetal HPCs that is relaxed during postnatal development. To resolve these possibilities, we used ATAC-seq, as well as H3K4me1, H3K27ac and H3K27me3 ChIP-seq, to identify cis-elements that putatively control FLT3ITD target gene expression in fetal and adult hematopoietic progenitor cells (HPCs). We identified many enhancer elements (ATAC-seq peaks with H3K4me1 and H3K27ac) that exhibited increased chromatin accessibility and activity in FLT3ITD adult HPCs relative to wild type adult HPCs. These elements were enriched near FLT3ITD target genes. HOMER analysis showed enrichment for STAT5, ETS, RUNX1 and IRF binding motifs within the FLT3ITD target enhancers, but motifs for temporally dynamic transcription factors were not identified. We cloned a subset of the enhancers and confirmed that they could synergize with their promoter to activate a luciferase reporter. For representative enhancers, STAT5 binding sites were required to activate the enhancer - as anticipated - and RUNX1 repressed enhancer activity. We tested whether accessibility or priming changed between fetal and adult stages of HPC development. FLT3ITD-dependent changes in chromatin accessibility were not observed in fetal HPCs, though the enhancers were primed early in development as evidenced by the presence of H3K4me1. Repressive H3K27me3 were not present at FLT3ITD target enhancers in either or adult HPCs. The data show that FLT3ITD target enhancers are demarcated early in hematopoietic development, long before they become responsive to FLT3ITD signaling. Repressive marks do not appear to create an epigenetic barrier to enhancer activation in the fetal stage. Instead, age-specific transcription factors are likely required to pioneer enhancer elements so that they can respond to STAT5 and other FLT3ITD effectors. Disclosures No relevant conflicts of interest to declare.

scholarly journals Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Alec Vallota-Eastman ◽  
Eleanor C. Arrington ◽  
Siobhan Meeken ◽  
Simon Roux ◽  
Krishna Dasari ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Environmental Stress ◽  
Regulatory Networks ◽  
Target Genes ◽  
Cell Attachment ◽  
Past Research ◽  
Reverse Transcriptases ◽  
Cellular Processes ◽  
Binding Domains ◽  
Signal Response

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

scholarly journals The Cochaperone p23 Differentially Regulates Estrogen Receptor Target Genes and Promotes Tumor Cell Adhesion and Invasion

2006 ◽  
Vol 26 (14) ◽  
pp. 5205-5213 ◽  
Author(s):  
Ellinor Oxelmark ◽  
Jennifer M. Roth ◽  
Peter C. Brooks ◽  
Steven E. Braunstein ◽  
Robert J. Schneider ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Estrogen Receptor Alpha ◽  
Target Genes ◽  
Regulatory Element ◽  
Gene Activation ◽  
Tumor Development ◽  
Tumor Cell Adhesion ◽  
Cellular Processes ◽  
Estrogen Response ◽  
Adhesion And Invasion

ABSTRACT The cochaperone p23 plays an important role in estrogen receptor alpha (ER) signal transduction. In this study, we investigated how p23 regulates ER target gene activation and affects tumor growth and progression. Remarkably, we found that changes in the expression of p23 differentially affected the activation of ER target genes in a manner dependent upon the type of DNA regulatory element. p23 overexpression enhanced the expression of the ER target genes cathepsin D and pS2, which are regulated by direct DNA binding of ER to estrogen response elements (ERE). In contrast, the expression of other target genes, including c-Myc, cyclin D1, and E2F1, to which ER is recruited indirectly through its interaction with other transcription factors remains unaffected by changes in p23 levels. The p23-induced expression of pS2 is associated with enhanced recruitment of ER to the ERE in the promoter, whereas ER recruitment to the ERE-less c-Myc promoter does not respond to p23. Intriguingly, p23-overexpressing MCF-7 cells exhibit increased adhesion and invasion in the presence of fibronectin. Our findings demonstrate that p23 differentially regulates ER target genes and is involved in the control of distinct cellular processes in breast tumor development, thus revealing novel functions of this cochaperone.

scholarly journals In Vivo Chromatin Accessibility Correlates With Gene Silencing in Drosophila

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1539-1549 ◽  
Author(s):  
Antoine Boivin ◽  
Jean-Maurice Dura
Keyword(s):  
Gene Silencing ◽  
Chromatin Structure ◽  
Dna Methyltransferase ◽  
Target Genes ◽  
Position Effect ◽  
Chromatin Accessibility ◽  
Polycomb Group ◽  
Position Effect Variegation ◽  
Direct Support

Abstract Gene silencing by heterochromatin is a well-known phenomenon that, in Drosophila, is called position effect variegation (PEV). The long-held hypothesis that this gene silencing is associated with an altered chromatin structure received direct support only recently. Another gene-silencing phenomenon in Drosophila, although similar in its phenotype of variegation, has been shown to be associated with euchromatic sequences and is dependent on developmental regulators of the Polycomb group (Pc-G) of gene products. One model proposes that the Pc-G products may cause a local heterochromatinization that maintains a repressed state of transcription of their target genes. Here, we test these models by measuring the accessibility of white or miniwhite sequences, in different contexts, to the Escherichia coli dam DNA methyltransferase in vivo. We present evidence that PEV and Pc-G-mediated repression mechanisms, although based on different protein factors, may indeed involve similar higher-order chromatin structure.

scholarly journals Strong gene activation with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator

2018 ◽  
Author(s):  
S Selma ◽  
J Bernabé-Orts ◽  
M Vazquez-Vilar ◽  
B Diego ◽  
M Ajenjo ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Target Genes ◽  
Wide Spectrum ◽  
Gene Activation ◽  
Binding Activity ◽  
Transcriptional Activators ◽  
Endogenous Factors ◽  
Activation Domains ◽  
Dna Binding Activity ◽  
Genome Wide

ABSTRACTSynthetic Biology (SynBio) aims at rewiring plant metabolic and developmental programs with orthogonal regulatory circuits. This endeavour requires new molecular tools able to interact with endogenous factors in a potent yet at the same time highly specific manner. A promising new class of SynBio tools that could play this function are the synthetic transcriptional activators based on CRISPR/Cas9 architecture, which combine autonomous activation domains (ADs) capable of recruiting the cell’s transcription machinery, with the easily customizable DNA-binding activity of nuclease-inactivated Cas9 protein (dCas9), creating so-called Programmable Transcriptional Activators (PTAs). In search for optimized dCas9-PTAs we performed a combinatorial analysis with seven different ADs arranged in four different protein/RNA architectures. This analysis resulted in the selection of a new dCas9-PTA with improved features as compared with previously reported activators. The new synthetic riboprotein, named dCasEV2.1, combines EDLL and VPR ADs using a multiplexable mutated version (v2.1) of the previously described aptamer-containing guide RNA2.0. We show here that dCasEV2.1 is a strong and wide spectrum activator, displaying variable activation levels depending on the basal activity of the target promoter. Maximum activation rates reaching up to 10000 fold were observed when targeting the NbDFR gene. Most remarkably, RNAseq analysis of dCasEV2.1-transformed N. benthamiana leaves revealed that the topmost activation capacity of dCasEV2.1 on target genes is accompanied with strict genome-wide specificity, making dCasEV2.1 an attractive tool for rewiring plant metabolism and regulatory networks.

The Gypsy Insulator of Drosophila Affects Chromatin Structure in a Directional Manner

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1649-1658
Author(s):  
Siquan Chen ◽  
Victor G Corces
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Protein A ◽  
Distal Region ◽  
Chromatin Accessibility ◽  
Chromatin Organization ◽  
Gypsy Insulator ◽  
Regulate Gene Expression ◽  
Hypersensitive Sites ◽  
Regulate Gene

Abstract Chromatin insulators are thought to regulate gene expression by establishing higher-order domains of chromatin organization, although the specific mechanisms by which these sequences affect enhancer-promoter interactions are not well understood. Here we show that the gypsy insulator of Drosophila can affect chromatin structure. The insulator itself contains several DNase I hypersensitive sites whose occurrence is dependent on the binding of the Suppressor of Hairy-wing [Su(Hw)] protein. The presence of the insulator in the 5′ region of the yellow gene increases the accessibility of the DNA to nucleases in the promoter-proximal, but not the promoter-distal, region. This increase in accessibility is not due to alterations in the primary chromatin fiber, because the number and position of the nucleosomes appears to be the same in the presence or absence of the insulator. Binding of the Su(Hw) protein to insulator DNA is not sufficient to induce changes in chromatin accessibility, and two domains of this protein, presumed to be involved in interactions with other insulator components, are essential for this effect. The presence of Modifier of mdg4 [Mod(mdg4)] protein, a second component of the gypsy insulator, is required to induce these alterations in chromatin accessibility. The results suggest that the gypsy insulator affects chromatin structure and offer insights into the mechanisms by which insulators affect enhancer-promoter interactions.

scholarly journals Role of Diversity-Generating Retroelements for Regulatory Pathway Tuning in Cyanobacteria

2020 ◽  
Author(s):  
Alec Vallota-Eastman ◽  
Eleanor C. Arrington ◽  
Siobhan Meeken ◽  
Simon Roux ◽  
Krishna Dasari ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Environmental Stress ◽  
Regulatory Networks ◽  
Target Genes ◽  
Cell Attachment ◽  
Past Research ◽  
Reverse Transcriptases ◽  
Cellular Processes ◽  
Binding Domains ◽  
Signal Response

AbstractBackgroundCyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes.ResultsMembers of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria.ConclusionWe find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

scholarly journals miRDRN—miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7309
Author(s):  
Hsueh-Chuan Liu ◽  
Yi-Shian Peng ◽  
Hoong-Chien Lee
Keyword(s):  
Web Service ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Mirna Target ◽  
Target Genes ◽  
Gene Annotation ◽  
Biological Pathways ◽  
Tissue Specific ◽  
Cellular Processes ◽  
Disease Pair

Background MicroRNA (miRNA) regulates cellular processes by acting on specific target genes, and cellular processes proceed through multiple interactions often organized into pathways among genes and gene products. Hundreds of miRNAs and their target genes have been identified, as are many miRNA-disease associations. These, together with huge amounts of data on gene annotation, biological pathways, and protein–protein interactions are available in public databases. Here, using such data we built a database and web service platform, miRNA disease regulatory network (miRDRN), for users to construct disease and tissue-specific miRNA-protein regulatory networks, with which they may explore disease related molecular and pathway associations, or find new ones, and possibly discover new modes of drug action. Methods Data on disease-miRNA association, miRNA-target association and validation, gene-tissue association, gene-tumor association, biological pathways, human protein interaction, gene ID, gene ontology, gene annotation, and product were collected from publicly available databases and integrated. A large set of miRNA target-specific regulatory sub-pathways (RSPs) having the form (T, G1, G2) was built from the integrated data and stored, where T is a miRNA-associated target gene, G1 (G2) is a gene/protein interacting with T (G1). Each sequence (T, G1, G2) was assigned a p-value weighted by the participation of the three genes in molecular interactions and reaction pathways. Results A web service platform, miRDRN (http://mirdrn.ncu.edu.tw/mirdrn/), was built. The database part of miRDRN currently stores 6,973,875 p-valued RSPs associated with 116 diseases in 78 tissue types built from 207 diseases-associated miRNA regulating 389 genes. miRDRN also provides facilities for the user to construct disease and tissue-specific miRNA regulatory networks from RSPs it stores, and to download and/or visualize parts or all of the product. User may use miRDRN to explore a single disease, or a disease-pair to gain insights on comorbidity. As demonstrations, miRDRN was applied: to explore the single disease colorectal cancer (CRC), in which 26 novel potential CRC target genes were identified; to study the comorbidity of the disease-pair Alzheimer’s disease-Type 2 diabetes, in which 18 novel potential comorbid genes were identified; and, to explore possible causes that may shed light on recent failures of late-phase trials of anti-AD, BACE1 inhibitor drugs, in which genes downstream to BACE1 whose suppression may affect signal transduction were identified.

scholarly journals Chromatin accessibility and histone acetylation in the regulation of competence in early development

2019 ◽  
Author(s):  
Melody Esmaeili ◽  
Shelby A. Blythe ◽  
John W. Tobias ◽  
Kai Zhang ◽  
Jing Yang ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Neural Crest ◽  
Target Genes ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Histone Deacetylase Inhibition ◽  
Inductive Signals

AbstractAs development proceeds, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner. While key inductive signaling pathways within competent cells are well-described at a molecular level, the mechanisms by which tissues lose responsiveness to inductive signals are not well understood. Localized activation of Wnt signaling before zygotic gene activation in Xenopus laevis leads to dorsal development, but competence to induce dorsal genes in response to Wnts is lost by the late blastula stage. We hypothesize that loss of competence is mediated by changes in histone modifications leading to a loss of chromatin accessibility at the promoters of Wnt target genes. We use ATAC-seq to evaluate genome-wide changes in chromatin accessibility across several developmental stages. Based on overlap with p300 binding, we identify thousands of putative cis-regulatory elements at the gastrula stage, including sites that lose accessibility by the end of gastrulation and are enriched for pluripotency factor binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence in the early gastrula while genes involved in mesoderm and neural crest development maintain accessibility at their promoters. Inhibition of histone deacetylases increases acetylation at the promoters of dorsal Wnt target genes and extends competence for dorsal gene induction by Wnt signaling. Histone deacetylase inhibition, however, is not sufficient to extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.

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